It seems to be different for everyone. The trick for this regimen is to try and be patient and eventually your skin should clear.
Congratulations on the improvements you've experienced so far, and if you change your way of looking at things - the last 12 weeks would have gone by regardless of whether you were following the regimen or not. At least you're over the awful first couple of months, so it can only keep improving from here.
Good luck and keep up all informed on your progress 
AHA certainly isnt necessary to the Regimen but it does help the appearance and texture of your skin if you find you can tolerate it.
I also broke out when I first started using it, but I kept with it because what I found it did was bring all the tiny tiny bumps that were under the surface of my skin (only noticeable if light hit my face a certain way) up to the top as tiny white heads. Once they healed up (took about 1 - 1.5 weeks) my skin was amazingly smooth. Every time I washed my face I just couldn't believe how my skin felt under my finger tips.
So even thought its not essential to use, you may want to reconsider trying it again.
Oh and another thing I was going to ask is if you've taken any progress photos. I know when I hit week 10, even though I was pretty happy with how my skin was progressing, I was still unhappy with how it was looking, until I reminded myself at how much my skin had improved when looking back at my original photos. We are our own worse critiques and often forget how far we've come.